############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Pigengene_1.32.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.32.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘Pigengene’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn") one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db * checking Rd files ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? 28 | {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.} | ^ checkRd: (-1) pigengene-class.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:30-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:77-79: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed one.step.pigengene 258.934 0.962 248.093 Pigengene-package 254.102 0.625 242.951 get.enriched.pw 85.974 2.432 88.703 module.heatmap 49.852 0.469 50.468 compute.pigengene 39.834 0.095 36.633 make.filter 26.809 0.163 25.323 apply.filter 25.703 0.024 23.913 plot.pigengene 21.366 0.093 19.878 pigengene 21.080 0.197 19.741 project.eigen 20.644 0.150 19.223 learn.bn 19.378 0.091 19.516 combine.networks 16.989 0.004 16.508 compact.tree 16.263 0.052 16.342 determine.modules 15.985 0.027 15.714 make.decision.tree 15.603 0.036 15.665 wgcna.one.step 15.292 0.008 14.999 gene.mapping 7.895 0.386 21.537 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/Pigengene.Rcheck/00check.log’ for details.